Biological soil crust (biocrust) communities of bacteria, fungi, lichen, algae, and bryophytes were recently shown to release nitrogen (N) to the crop root zone in agroecosystems. While biocrusts in semi‐arid and dryland ecosystems have neutral, negative, and facilitative effects on plants, it is not known how agroecosystem biocrusts affect crop N accumulation and growth. Like biocrusts, legume cover crop associations with N‐fixing bacteria can increase soil N after termination, potentially supporting primary crops. This research compared the effects of biocrust application to a legume cover crop (cowpea; Vigna unguiculata) on citrus (Citrus sinensis) rootstock seedling growth, root system, and N accumulation. Seedling biomass, N accumulation, and stable N isotopic ratios (δ15N) were quantified after 29 and 120 d. Sampling date and amendment type had significant effects on seedling biomass, N content, root biomass distributions, and δ15N (p < .05). Seedlings with cowpea had less biomass than seedlings with biocrust or no amendment after 29 d. After 120 d, seedlings with biocrusts had significantly less biomass than seedlings with cowpea or no amendment (p < .05). Furthermore, seedlings without an amendment had significantly greater total root length than seedlings with an amendment (p < .05). Seedlings with biocrust had significantly less total N than seedlings with cowpea or no amendment despite having significantly lower plant δ15N (p < .05). These δ15N values indicated biocrust and cowpea were potentially N sources for seedlings. Overall, cowpea initially inhibited seedling growth, and biocrust had neutral and negative effects on seedling growth after 120 d.